TCP Max Segment size vs Window size and WAAS

TCP maximum segment size is the size of a packet that is sent from one host to another. It is set as a flag during TCP session establishment. It is MTU minus 40 bytes. With that being said, I am very confused about Window size in WAAS. If MSS is always less than MTU, how can we get up to 1Million byte window? I had always assumed that the 1million byte window was broken up into MTU size packets as it is sent. But if anyone knows the mechanics of how these interrelate, I am more than curious.